In this paper, a novel state-estimator-integrated robust adaptive tracking control law is proposed for flexible air-breathing hypersonic vehicle (FAHV), with consideration of noisy measurements, parametric uncertainties, and unknown flexible dynamics. First, to reconstruct the states contaminated by the measurement noises, a continuous-model-based state estimator is designed, which can avoid severe phase lag problem brought by low-pass filter and greatly improve the estimation accuracy in the transition process. Then, based on noise-free measurements, an ideal state feedback robust adaptive tracking controller is formulated to deal with the parametric uncertainties as well as unknown flexible dynamics, where interval type-2 fuzzy logic systems are employed to approximate the unknown dynamics of FAHV online. Lyapunov theorem is utilized to analyze the stability properties of the state estimator and the ideal state feedback tracking controller. By synthesizing the above two parts, the whole state-estimator-integrated robust adaptive tracking control law is finally developed. Comparative numerical simulations of four scenarios demonstrate the effectiveness and superiority of the proposed integrated control law.